Considerable attention is paid to the opportunities of using these approaches to detect DNA polymorphism in the form of converting the obtained data to digital format and creation of integrative databases for all organisms, regardless of the methods used.įor citation: Kuluev B.R., Baymiev An.Kh., Gerashchenkov G.A., Chemeris D.A., Zubov V.V., Kuluev A.R., Baymiev Al.Kh., Chemeris A.V. Another approach for revealing polymorphism that does not require knowledge of the DNA sequence is based on cleavage of total DNA by a combination of restriction endonucleases (random cleavage) accompanied by PCR amplification. Another group of methods to detect DNA polymorphism is based on the use of primers that consist of short repetitive sequences having anchor nucleotides at the 5'- or 3'-ends that position the annealing sites of these primers (microsatellite priming).
The first group of these methods includes approaches based on the use of primers with arbitrary sequence (random priming). Overall, although many initiatives to improve data access have been started in the research community, their impact on the availability of datasets underlying published articles remains unclear to date.Ī historical review of the advent and improvement of the methods for detecting multilocus DNA polymorphism that do not require preliminary knowledge of the individual gene and complete genome sequences of eukaryotes is presented. In the discussion, we present recommendations on how veterinary research could move towards greater reusability according to FAIR principles. Interoperability, in particular, requires specific skills in data management which may not yet be broadly available in the epidemiology community. None of the datasets assessed in this study met all the requirements set by the FAIR principles. The available data objects generally scored favourably for Findable, Accessible and Reusable indicators, but Interoperability was more problematic. Data availability was much higher for molecular epidemiology papers, in line with a strong repository base available to scientists in this discipline. Consistent with previous assessments conducted in other disciplines, our results showed that most datasets used in non-molecular epidemiological studies were not available (i.e., neither findable nor accessible). We considered the differences in practices between molecular epidemiology, the branch of epidemiology using genetic sequences of pathogens and hosts to describe disease patterns, and non-molecular epidemiology.Ī total of 152 articles were included in the assessment. In this systematic review, we assessed the FAIRness of datasets associated with peer-reviewed articles in veterinary epidemiology research published since 2017, specifically looking at salmonids and dairy cattle. The FAIR (Findable, Accessible, Interoperable, Reusable) principles were proposed in 2016 to set a path towards reusability of research datasets. This suggests that emerging outbreaks of AGD are not due to rapid translocation of this important salmonid pathogen from the same area. While genetic differences were identified between geographical isolates, a BURST analysis provided no evidence of a founder genotype. perurans from Tasmania, Australia were more similar to each other than to the isolates from other countries. Both techniques consistently identified that isolates of N. Genetic polymorphism among isolates was more evident from the RAPD analysis compared to the MLST that used conserved housekeeping genes. All the samples from Australia came from farm sites on the island state of Tasmania. These analyses were applied to a total of 16 isolates from Australia, Canada, Ireland, Scotland, Norway, and the USA. perurans with the objective of distinguishing geographical isolates. To the best of our knowledge, this study represents the first use of these typing methods applied to N. Multilocus sequence typing (MLST) and Random Amplified Polymorphic DNA (RAPD) are PCR-based typing methods that allow for the highly reproducible genetic analysis of population structure within microbial species. Neoparamoba perurans, is the aetiological agent of amoebic gill disease (AGD), a disease that affects farmed Atlantic salmon worldwide.
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